In Roger Goodell’s nearly decade-long zeal to establish order in the National Football League, he has handed down penalties for everything from domestic violence to dogfighting to deflating footballs.

But as was made apparent again Thursday, when a federal judge threw out a four-game suspension he assessed against the league’s biggest star, New England Patriots quarterback Tom Brady, the commissioner continues to stumble in policing America’s most popular sport and making the tough calls stick. Goodell had suspended Brady in connection with accusations that he played a role in deflating footballs for competitive advantage in a January championship game.

Like his predecessors in the N.F.L. and in other leagues, who for decades have had broad powers to protect the integrity of their sports, Goodell has made progress prosecuting players for using steroids, recreational drugs and other banned substances detectable with science.

But when it comes to punishing players for criminal behavior or cheating on the field, Goodell has faced far stiffer opposition and has a spotty record.

Players armed with high-priced lawyers and publicists, and backed by a players’ union led by a former prosecutor, have mined sometimes arcane labor law to argue they were denied due process and to resist Goodell’s self-proclaimed goals to rein in misconduct.

“It really is exceptional how the federal courts have taken on the role of super-arbitrator of the N.F.L.’s disciplinary standards,” said Michael LeRoy, a sports labor law specialist at the University of Illinois, Urbana-Champaign. “Commissioners have traditionally been godlike authorities dating back to Judge Kenesaw Mountain Landis. The fact that you can go to court and get a judge to tell the commissioner what he can and can’t do is extraordinary. It feels there are three parties at the bargaining table: the N.F.L., the union and the courts.”

The Brady case is emerging as the most vivid example of Goodell’s efforts and their pitfalls.

In vacating Brady’s suspension, handed down in May after a league investigative report determined the quarterback was most likely aware that two team equipment staff members had deflated balls in an apparent bid to give him a better grip on them, Judge Richard M. Berman of Federal District Court in Manhattan did not focus on whether Brady had tampered with the game balls. He did not question the outcome of the game, a 45-7 Patriots victory over the Indianapolis Colts as the team marched on to win the Super Bowl.

Instead, he focused on the narrower question of whether the collective bargaining agreement between the N.F.L. and the players’ union gave Goodell the authority to carry out the suspension, and whether Brady was treated fairly during his attempt to overturn the punishment.

Judge Berman, in a 40-page decision that the N.F.L. has indicated it plans to appeal, found several “significant legal deficiencies” in the N.F.L. case. He ruled that Brady was not treated fairly and could not be suspended for deflating footballs because he was not aware such misconduct could lead to the kind of punishment he received.

“General awareness” of others’ misconduct, a reference to equipment handlers who may have actually deflated the balls, was not enough to suspend him, the judge said.

“The court finds that Brady had no notice that he could receive a four-game suspension for general awareness of ball deflation by others or participation in any scheme to deflate footballs, and noncooperation with the ensuing investigation,” Berman wrote.

“No N.F.L. policy or precedent notifies players that they may be disciplined (much less suspended) for general awareness of misconduct by others,” he added.

Even if the league believed Brady had obstructed the investigation, by having a cellphone destroyed before it could be fully examined, as the N.F.L. asserted he had done, the judge sided with Brady’s argument that “there is no evidence of a record of past suspensions based purely on obstructing a league investigation.”

He found that the N.F.L. did not give Brady adequate notice of the potential penalty for the misconduct he was accused of and that he had been denied sufficient access to the N.F.L.’s investigative files and to a top league legal official reviewing the case.

The way is cleared for Brady to play in the Patriots’ opening game Sept. 10 against the Pittsburgh Steelers in Foxborough, Mass. Already, the case had made for a protracted spectacle pored over and at times ridiculed on social media. There was the morning Brady, a player most likely bound for the Hall of Fame, walked into the sober confines of a federal courthouse in Manhattan — with the ensuing jostle of the paparazzi and even a courtroom sketch that many felt maligned him and caused an Internet sensation. The judge himself at one point seemed to wonder if there were not more important matters in the world.

Now, the N.F.L. may brace for a nationally televised hero’s welcome for Brady accepting adulation from hometown fans not just for winning last season’s Super Bowl, but for winning what at times has seemed like a personal showdown between the commissioner and one of his most marketable players.

If Goodell thought he could win the day in court, he may have to rethink the strategy or take the chance that appellate judges might be more sympathetic on further review.

In recent years, judges have found themselves enmeshed in cases involving players suspended for beating their children, punching their girlfriends and other criminal behavior far removed from the field of play. In the N.F.L., many of these cases fall under the personal conduct policy that legal experts say often falls short of clarity. This has allowed Goodell to penalize players, but also left him exposed to allegations that he has abused his powers.

Lawyers are split on how the United States Court of Appeals for the Second Circuit might rule. The league may argue that the labor agreement gives the commissioner wide latitude to take action against misconduct, even if his methods are imperfect, logic that judges have used to uphold the vast majority of arbitration rulings.

But the appeals court may also agree with Berman, said Mark Conrad, who teaches sports law at Fordham University, because of all the procedural flaws he identified in the league’s handling of the case.

Both sides will closely watch a pending case in the Eighth Circuit, which is considering the N.F.L.’s request to overturn a lower court decision that effectively ended the suspension of Minnesota Vikings running back Adrian Peterson stemming from a child abuse charge related to his disciplining his young son.

In other high-profile cases, appeals have not gone Goodell’s way.

His suspension of New Orleans Saints players who purportedly earned a “bounty” for hurting rivals was overturned in 2012 by his predecessor, the former commissioner Paul Tagliabue, whom the league had appointed to handle appeals.

In the past year, a former federal judge, who had been appointed as arbitrator, chastised Goodell for suspending Ray Rice, the former Baltimore running back, twice for the same penalty.

In July, a league-appointed arbitrator reduced the suspension of Dallas Cowboys defensive end Greg Hardy to four games from 10 in a domestic violence case.

Still, few suggest Goodell’s job is in jeopardy, however queasy owners may be about his tactics.

“The owners are behind him, but they want to find a better approach so that neither the commissioner nor the shield take as many hits,” said Marc Ganis, an adviser to several owners. “When the office of the commissioner is in the eye of the storm, it can distract from operating and advancing the league.”

New England fans, of course, have a different view. Rarely had a preseason game generated the kind of excitement that Thursday night’s did, knowing the starting quarterback would soon be back.

“I think he realized Mr. Goodell dug himself a hole and he didn’t have a shovel to dig himself out,” Philip Rowe of Chicopee, Mass., said, referring to Berman. “He was wrong on Ray Rice, he was wrong here, and I think people have had enough of Mr. Goodell.”

Tom Pedulla contributed reporting from Foxborough, Mass.

A version of this article appears in print on , Section A, Page 1 of the New York edition with the headline: N.F.L.’s Leader Finds Authority Is Not Absolute. Order Reprints | Today’s Paper | Subscribe